Well, technically you do nuke the entire population when you take a planet. So traders would be the only ones left to revolt.
Even if you are Advent? Even in your logic there is a fail here, if you wipe out the total population, and your ADVENT citizens fill the planet, then how is it possible 1. they will revolt against you (they are loyal to you..) 2. and as TEC rebels?
I don't think you bomb the entire population, I always thought you only bomb the floating cities of the occupying civilization, not the natives who have those nice city lights around the planet. No race would have the advantage from wiping out billions of people, especially Vasari Loyalists who like to slave inferiors, or Advent who may find new followers among that newly acquired billions of humans.